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High correlation observed between replicates of samples in present study.
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A >threefold difference cutoff was >sixfold the standard deviation between replicates of all samples and was therefore highly significant.
Correlations of expression profiles among technical replicates of three times amplified samples range between 0.977 and 0.994 and thus is in the range of what was previously reported between technical replicates of samples processed with only one linear amplification (Zakharkin et al. 2005).
While large regions with a single genotype were consistent with some minor variation in imputed breakpoint position, the genotype of smaller regions varied between some replicates of samples covered in both the HincII and RsaI datasets (Additional file 8: Figure S7).
In order to show the specificity of the correlation between replicates of the same sample and between the FFPE/FF paired samples, we also report the average correlation of each sample against all other non-replicate/non-pair samples.
These correlations are comparable to the correlation observed between replicates of the untreated samples (τ = 0.70; Spearman's rank correlation; Table S1), suggesting that drug-induced silencing of transcription has minor impact on DNA contacts formed by the β-globin locus.
CD14+ monocyte gene expression profiles measured in three individuals three months apart show a strong correlation (R2 = 0.83 ± 0.06, [see Additional file 3B]) which is of a similar magnitude to that seen between replicates of the same sample, and greater than that seen between samples from different individuals (R2 = 0.83 ± 0.03 and R2 = 0.73 ± 0.06, respectively, [see Additional file 3A and 3C]).
To assess variation in the qualitative measures, the percentage of 309 microRNAs with concordant detection calls between replicates of the same sample type was calculated on each platform (line graphs in Figure 4A).
There was a high concordance between replicates of the same sample (data not shown).
Our estimation of targeted RNA fraction is imperfect; an assumption of the model we built is that the enrichment proportion is constant between replicates of the same sample.
Four biological replicates of samples were prepared.
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